Several indigenous cattle breeds in Sweden are endangered. Conservation of their genetic diversity and genomic characterization is a priority.Whole-genome sequences (WGS) with a mean coverage of 25X, ranging from 14 to 41X were obtained for 30 individuals of the breeds Fjällko, Fjällnära, Bohuskulla, Rödkulla, Ringamåla, and Väneko. WGS-based genotyping revealed 22,548,028 variants in total, comprising 18,876,115 single nucleotide polymorphisms (SNPs) and 3,671,913 indels. Out of these, 1,154,779 SNPs and 304,467 indels were novel. Population stratification based on roughly 19 million SNPs showed two major groups of the breeds that correspond to northern and southern breeds. Overall, a higher genetic diversity was observed in the southern breeds compared to the northern breeds. While the population stratification was consistent with previous genome-wide SNP array-based analyses, the genealogy of the individuals inferred from WGS based estimates turned out to be more complex than expected from previous SNP-array based estimates. Polymorphisms and their predicted phenotypic consequences were associated with differences in the coat color phenotypes between the northern and southern breeds. Notably, these high-consequence polymorphisms were not represented in SNP arrays, which are used routinely for genotyping of cattle breeds.This study is the first WGS-based population genetic analysis of Swedish native cattle breeds. The genetic diversity of native breeds was found to be high. High-consequence polymorphisms were linked with desirable phenotypes using whole-genome genotyping, which highlights the pressing need for intensifying WGS-based characterization of the native breeds.
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http://dx.doi.org/10.1186/s12864-024-09959-9 | DOI Listing |
Exp Appl Acarol
January 2025
Laboratorio de Vectores y Enfermedades Transmitidas, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Salto, Uruguay.
Babesia species (Piroplasmida) are hemoparasites that infect erythrocytes of mammals and birds and are mainly transmitted by hard ticks (Acari: Ixodidae). These hemoparasites are known to be the second most common parasites infecting mammals, after trypanosomes, and some species may cause malaria-like disease in humans. Diagnosis and understanding of Babesia diversity increasingly rely on genetic data obtained through molecular techniques.
View Article and Find Full Text PDFGenes Genomics
January 2025
Department of Pediatric Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, Henan, China.
Background: The clinical course of high-risk neuroblastoma patients remains suboptimal, and the dynamic and reversible nature of cellular senescence provides an opportunity to develop new therapies.
Objective: This study aims to identify unique markers of cellular senescence in neuroblastoma and to explore their clinical significance.
Methods: The impact of multiple genetic regulatory mechanisms on cellular senescence-associated genes (CSAGs) was first assessed.
Theor Appl Genet
January 2025
USDA, ARS, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC, 29414, USA.
Complex traits influenced by multiple genes pose challenges for marker-assisted selection (MAS) in breeding. Genomic selection (GS) is a promising strategy for achieving higher genetic gains in quantitative traits by stacking favorable alleles into elite cultivars. Resistance to Fusarium oxysporum f.
View Article and Find Full Text PDFSci Rep
January 2025
Yunnan Provincial Key Laboratory of Children's Major Diseases Research, School of Basic Medicine, Kunming Medical University, Kunming, 650500, China.
This study focused on the relationships among gut microbiota, plasma protein ratios, and tuberculosis. Given the unclear causal relationship between gut microbiota and tuberculosis and the scarcity of research on relevant plasma protein ratios in tuberculosis, Mendelian randomization analysis (MR) was employed for in-depth exploration. By analyzing the GWAS data of individuals with European ancestry (the FinnGen dataset included 409,568 controls and 2613 cases), using the two-sample MR method, we focused on evaluating the impact of immunocyte-mediated gut microbiota on tuberculosis and the associations between 2821 plasma protein-to-protein ratios and tuberculosis.
View Article and Find Full Text PDFSci Rep
January 2025
Division for Neurogeriatrics, Centre for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden.
Copy number variation (CNV) of the amyloid-β precursor protein gene (APP) is a known cause of autosomal dominant Alzheimer disease (ADAD), but de novo genetic variants causing ADAD are rare. We report a mother and daughter with neuropathologically confirmed definite Alzheimer disease (AD) and extensive cerebral amyloid angiopathy (CAA). Copy number analysis identified an increased number of APP copies and genome sequencing (GS) revealed the underlying complex genomic rearrangement (CGR) including a triplication of APP with two unique breakpoint junctions (BPJs).
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